Miguel Hernandez-Prieto, Ravi Kalathur and Matthias E. Futschik (2014) Molecular networks, their analysis and representation, Chapter 24, 399-418, , Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer
Thomas Wallach, Katja Schellenberg, Bert Maier, Ravi Kalathur , Pablo Porras, Erich E. Wanker, Matthias E. Futschik and Achim Kramer (2013) Dynamic Circadian Protein-Protein Interaction Networks Predict Temporal Organization of Cellular Functions, PloS Genetics , 9(3): e1003398. doi:10.1371/journal.pgen.1003398 (html, pdf)
Ravi Kalathur, Miguel Hernandez-Prieto and Matthias E. Futschik (2012) Huntington´s Disease and its target genes: A global functional profile based on the HD Research Crossroads database, BMC Neurology , 12:47 (abstract)
Gürkan Bal, Julian Kamhieh-Milz, Tayseer Zaid, Matthias Futschik, Thomas Häupl, Abdulgabar Salama and Anja Moldenhauer (2012) Molecular profiling of the haematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVEC), Cell Transplantation 21(1):251-67( pdf)
Gautam Chaurasia and Matthias E. Futschik (2012) The Integration and Annotation of the Human Interactome in the UniHI Database Methods in Molecular Biology 812: 175-188 (PubMed, pdf)
C. T. Duong, L. Strack, M. Futschik, Y. Katou, Y. Nakao, T. Fujimura, K. Shirahige, Y. Kodama, E. Nevoigt (2011) Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast, Metabolic Engineering, 13(6):638-47 (PubMed, pdf)
Anja Moldenhauer, Matthias Futschik, Huili Lu, Melanie Helmig, Patricc Götze, Gürkan Bal, Martin Zenke,Wei Han an Abdulgabar Salama (2011) Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity, European Journal of Immunology, 41(6):1774-86 (pdf)
Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias Futschik and Enrico Capobianco (2010) Inferring modules from human protein interactome classes, BMC Systems Biology, 4:102 (pdf, html)
Jenny Russ and Matthias E. Futschik (2010) Comparison and consolidation of microarray data sets of human tissue expression, BMC Genomics (pdf,html)
Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen and Sallie W. Chisholm (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus, Genome Biology (pdf,html)
Gautam Chaurasia and Matthias E. Futschik (2009) Interactomics and Cancer, An Omics Perspective of Cancer, eds. W. Cho, Springer, Chapter 5: 167- 182 (pdf)
Michael J. Allen, Bela Tiwari, Matthias E. Futschik and Debbie Lindell (2009) Methods in aquatic virus ecology: Construction of microarrays and their application to virus analysis, Manual of Aquatic Viral Ecology, American Society of Limnology and Oceanography, Chapter 5: 34–56 (pdf)
E.R. Zinser, D. Lindell, Z.I.Johnson, M.E. Futschik, C. Steglich, M.L. Coleman, M.A. Wright, T. Rector, R. Steen, N, McNulty, L.R. Thompson and S.W. Chisholm (2009) Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus, PlosONE, 4(4): e5135. doi:10.1371/journal.pone.0005135 (pdf)
Matthias Futschik, Wolfgang Kemmner, Reinhold Schäfer and Christine Sers (2009) The Human Transcriptome: Implications for the Understanding of Human Diseases, Molecular Pathology, eds. W.B. Coleman and G. Tsongalis, Academic Press, Elsevier, Chapter 7 :123-150 (pdf)
Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian. Hänig, Erich. E. Wanker and Matthias. E. Futschik. (2009) UniHI 4: New tools for query, analysis and visualization of the human protein-protein interactome, Nucleic Acids Research, 37, Database issue: D657-D660 (pdf)
Jörg Gsponer, Matthias E. Futschik, Sarah A. Teichmann and M. Madan Babu (2008) Tight regulation of intrinsically unstructured proteins: from transcript synthesis to protein degradation, Science, 322, 1365-1368 (pdf)
Claudia Steglich, Matthias E. Futschik, Debbie Lindell, Bjoern Voss, Sallie W. Chisholm and Wolfgang R. Hess (2008) The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus, Plos Genetics 4(8): e1000173 (pdf)
Matthias E. Futschik and Hanspeter Herzel (2008) Are we overestimating the number of cell-cycling genes? The impact of background models on time series analysis, Bioinformatics, 24(8):1063-1069 (pdf)
Matthias E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu and Hanspeter Herzel (2007) Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network, Journal of Integrative Bioinformatics, 4(3):76 (pdf)
Matthias Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Genome Informatics, 18, 141-15 (pdf)
D. Lindell, J. Jaffe, M. Coleman, M. Futschik, I. Axmann, T. Rector, G. Kettler, M. Sullivan, R. Steen, W. Hess, G. Church and S. Chisholm (2007) Genome-Wide Expression Dynamics of a Marine Virus and its Host Reveal Features of Co-evolution, Nature, 449, 83 - 86 (pdf)
P. Umbach, M. Futschik, U.Stelzl and E.Wanker (2007) Funktion durch Netzwerke von Proteinen und ihren Wechselwirkungen, Laborwelt, 8(2):9-11 (ps)
L. Kumar and M.E. Futschik (2007) Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2(1) 5-7 (pdf)
Matthias Futschik, Gautam Chaurasia, and Hanspeter Herzel (2007) Comparison of human protein-protein interaction maps, Bioinformatics, 23(5):605-611 (pdf)
G. Chaurasia, C. Hänig, Y. Iqbal, H. Herzel, E.Wanker and M. E. Futschik (2007) Flexible web-based integration of distributed large-scale interaction data sets, Journal of Integrative Bioinformatics, 4(1) (pdf)
G. Chaurasia, Y. Iqbal, C. Hänig, H. Herzel, E. E. Wanker and M. E. Futschik (2007) UniHI: An Entry Gate to the Human Protein Interactome, Nucleic Acids Research Database issue, 35, D590-4 (pdf)
C. Steglich, M. Futschik, T. Rector and S.W. Chisholm (2006) Genome-wide analysis of light sensing in Prochlorococcus, Journal of Bacteriology, 188(22):7796-806 (pdf)
Gautam Chaurasia, Hanspeter Herzel, Erich Wanker and Matthias E. Futschik (2006) Systematic functional assessment of human protein interaction maps, Genome Informatics, 17(1), 36-45. (pdf)
L. Kumar, M. Futschik and H. Herzel (2006) DNA motifs and sequence periodicities, In Silico Biology, 6, 0008 (html)
M.E. Futschik and B. Charlisle (2005) Noise robust soft clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-98 (pdf)
M.E. Futschik and T. Crompton (2005) OLIN: optimized normalization, visualization and quality testing of two-channel microarray data, Bioinformatics, 21(8):1724-6 (pdf)
M. Futschik and T. Crompton (2004) Model selection and efficiency testing for normalization of cDNA microarray, Genome Biology, 5(8):R60 (pdf)
M.E. Futschik, M. Sullivan, A. Reeve, N. Kasabov (2003) Prediction of clinical behaviour and treatment for cancers, Applied Bioinformatics, 3(2): S53-58 (pdf)
M.E. Futschik, A. Reeve and N. Kasabov (2003) Evolving connectionist systems for knowledge discovery from gene expression data of gene expression data of cancer tissue, Artificial Intelligence in Medicine, 28: 165-189, 2003 (pdf)
M.E. Futschik and N.K. Kasabov (2002). Fuzzy clustering of gene expression data, Proceedings of World Congress of Computational Intelligence WCCI 2002, IEEE Press.(pdf)
B. Humar, F. Graziano, S. Cascinu, V. Catalano, A.M. Ruzzo, M. Magnani, T. Turo, M.E. Futschik, T.Merriman and P. Guilford, (2002) Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer, Oncogene, 21(53): 8192-8195 (pdf)
M. Futschik, A. Jeffs, S. Pattison, N. Kasabov, M. Sullivan, A. Merrie and A. Reeve (2002) Gene expression profiling of metastatic and non-metastatic colorectal cancer cell-lines, Genome Letters, vol.1, No.1, 26-34 (pdf)
C. Brown, G. Jacobs, M. Schreiber, J. Magnum, J. McNaughton, M. Cambray, M. Futschik, Major, O. Rackham, W. Tate, P. Stockwell, C. Thompson and N. Kasabov, (2000) Using bioinformatics to investigate post-transcriptional control of gene expression, NZ Bio Science, 7(4), 11-12